Computer-assisted interpretation, in-depth exploration and single cell type annotation of RNA sequence data using k-means clustering algorithm

Pranshu Saxena, Amit Sinha and Sanjay Kumar Singh

Computer Methods in Biomechanics and Biomedical Engineering, 2025, vol. 28, issue 5, 668-678

Abstract: At now, the majority of approaches rely on manual techniques for annotating cell types subsequent to clustering the data obtained from single-cell RNA sequencing (scRNA-seq). These approaches require a significant amount of physical exertion and depend substantially on the user’s skill, perhaps resulting in uneven outcomes and inconsistency in treatment. In this paper, we provide a computer-assisted interpretation of every single cell of a tissue sample, along with an in-depth exploration of an individual cell’s molecular, phenotypic and functional attributes. The paper will also perform k-means clustering followed by silhouette validation based on similar phenotype and functional attributes, and also, cell type annotation is performed, where we match a cell’s gene profile against some known database by applying certain statistical conditions. Finally, all the genes are mapped spatially on the tissue sample. This paper is an aid to medicine to know which cells are expressed/not expressed in a tissue sample and their spatial location on the tissue sample.

Date: 2025
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DOI: 10.1080/10255842.2023.2300685

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